6c567fd9a03e87610681a43d2183ebb43547d1ad
lrnassar
  Fri Apr 24 17:58:57 2026 -0700
PromoterAI: review followups. refs #37278

Move /gbdb/hg38/promoterAi/ to /gbdb/hg38/_promoterAi/ to match the
underscore-prefix exclusion rule for hgdownload sync (same pattern as
PrimateAI-3D under refs #37274). bigDataUrls and the makedoc updated.

Bump bigWig maxHeightPixels from 128:20:8 to 128:40:8 -- the peer-track
default of 20 is too cramped for a signed -1..+1 score.

Description page: drop the wrong primateai3d.basespace.illumina.com link
in Data Access; PromoterAI is not on BaseSpace, it's distributed via the
license agreement on the GitHub page (a download link is emailed after
submission). Reword Data Access and Methods accordingly.

Description page: add Illumina's recommended interpretation thresholds
(|score| >= 0.1, >= 0.2, >= 0.5) from the PromoterAI GitHub README, with
a note that higher cutoffs select smaller, higher-confidence sets.

diff --git src/hg/makeDb/trackDb/human/promoterAi.ra src/hg/makeDb/trackDb/human/promoterAi.ra
index 361816b51cb..216e1515711 100644
--- src/hg/makeDb/trackDb/human/promoterAi.ra
+++ src/hg/makeDb/trackDb/human/promoterAi.ra
@@ -1,99 +1,99 @@
 track promoterAi
 shortLabel PromoterAI
 longLabel PromoterAI Promoter Variant Impact Scores (zoom for exact score)
 type bigWig
 parent predictionScoresSuper
 compositeTrack on
 tableBrowser off
 visibility hide
 
         track promoterAiA
         shortLabel Mutation: A
         longLabel PromoterAI: Mutation is A
         type bigWig
         parent promoterAi on
         visibility dense
-        bigDataUrl /gbdb/$D/promoterAi/a.bw
-        maxHeightPixels 128:20:8
+        bigDataUrl /gbdb/$D/_promoterAi/a.bw
+        maxHeightPixels 128:40:8
         viewLimits -1:1
         viewLimitsMax -1:1
         maxWindowToDraw 10000000
         maxWindowToQuery 500000
         mouseOverFunction noAverage
         alwaysZero on
         autoScale off
         color 200,0,0
         altColor 0,0,200
 
         track promoterAiC
         shortLabel Mutation: C
         longLabel PromoterAI: Mutation is C
         type bigWig
         parent promoterAi on
         visibility dense
-        bigDataUrl /gbdb/$D/promoterAi/c.bw
-        maxHeightPixels 128:20:8
+        bigDataUrl /gbdb/$D/_promoterAi/c.bw
+        maxHeightPixels 128:40:8
         viewLimits -1:1
         viewLimitsMax -1:1
         maxWindowToDraw 10000000
         maxWindowToQuery 500000
         mouseOverFunction noAverage
         alwaysZero on
         autoScale off
         color 200,0,0
         altColor 0,0,200
 
         track promoterAiG
         shortLabel Mutation: G
         longLabel PromoterAI: Mutation is G
         type bigWig
         parent promoterAi on
         visibility dense
-        bigDataUrl /gbdb/$D/promoterAi/g.bw
-        maxHeightPixels 128:20:8
+        bigDataUrl /gbdb/$D/_promoterAi/g.bw
+        maxHeightPixels 128:40:8
         viewLimits -1:1
         viewLimitsMax -1:1
         maxWindowToDraw 10000000
         maxWindowToQuery 500000
         mouseOverFunction noAverage
         alwaysZero on
         autoScale off
         color 200,0,0
         altColor 0,0,200
 
         track promoterAiT
         shortLabel Mutation: T
         longLabel PromoterAI: Mutation is T
         type bigWig
         parent promoterAi on
         visibility dense
-        bigDataUrl /gbdb/$D/promoterAi/t.bw
-        maxHeightPixels 128:20:8
+        bigDataUrl /gbdb/$D/_promoterAi/t.bw
+        maxHeightPixels 128:40:8
         viewLimits -1:1
         viewLimitsMax -1:1
         maxWindowToDraw 10000000
         maxWindowToQuery 500000
         mouseOverFunction noAverage
         alwaysZero on
         autoScale off
         color 200,0,0
         altColor 0,0,200
 
         track promoterAiOverlaps
         shortLabel PromoterAI overlaps
         longLabel PromoterAI: Positions with >1 score due to overlapping transcripts
         type bigBed 9 +
         parent promoterAi on
         visibility dense
-        bigDataUrl /gbdb/$D/promoterAi/overlaps.bb
+        bigDataUrl /gbdb/$D/_promoterAi/overlaps.bb
         mouseOverField _mouseOver
         itemRgb on
         maxWindowToDraw 10000000
         maxItems 50000
         filterByRange.scoreDiff on
         filter.scoreDiff 0.01
         filterLimits.scoreDiff 0:2
         filterLabel.scoreDiff Minimum score difference across transcripts
         scoreFilter 0
         scoreFilterLimits 0:1000
         scoreLabel Absolute PromoterAI score * 1000